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- PDB-3tar: Crystal Structure of Bacillus DNA Polymerase I Large Fragment Bou... -

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Basic information

Entry
Database: PDB / ID: 3tar
TitleCrystal Structure of Bacillus DNA Polymerase I Large Fragment Bound to Duplex DNA with Cytosine-Adenine Mismatch at (n-6) Position
Components
  • 5'-D(*GP*AP*CP*GP*TP*AP*CP*GP*TP*GP*AP*TP*CP*GP*CP*A)-3'
  • 5'-D(*GP*CP*GP*AP*TP*CP*AP*CP*GP*CP*AP*CP*GP*TP*C)-3'
  • DNA polymerase I
KeywordsTRANSFERASE/DNA / DNA polymerase I / protein-DNA complex / TRANSFERASE-DNA complex
Function / homology
Function and homology information


Taq DNA Polymerase; Chain T, domain 4 / Taq DNA Polymerase; Chain T, domain 4 / Alpha-Beta Plaits - #370 / 5' to 3' exonuclease, C-terminal subdomain / Ribonuclease H-like superfamily/Ribonuclease H / DNA polymerase; domain 1 / Nucleotidyltransferase; domain 5 / Alpha-Beta Plaits / Up-down Bundle / 2-Layer Sandwich ...Taq DNA Polymerase; Chain T, domain 4 / Taq DNA Polymerase; Chain T, domain 4 / Alpha-Beta Plaits - #370 / 5' to 3' exonuclease, C-terminal subdomain / Ribonuclease H-like superfamily/Ribonuclease H / DNA polymerase; domain 1 / Nucleotidyltransferase; domain 5 / Alpha-Beta Plaits / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
sucrose / DNA / DNA (> 10) / :
Similarity search - Component
Biological speciesGeobacillus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.6 Å
AuthorsWang, W. / Beese, L.S.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Structural evidence for the rare tautomer hypothesis of spontaneous mutagenesis.
Authors: Wang, W. / Hellinga, H.W. / Beese, L.S.
#1: Journal: Cell(Cambridge,Mass.) / Year: 2004
Title: Structures of mismatch replication errors observed in a DNA polymerase.
Authors: Johnson, S.J. / Beese, L.S.
History
DepositionAug 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2011Group: Database references
Revision 1.2Apr 2, 2014Group: Source and taxonomy
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase I
B: 5'-D(*GP*CP*GP*AP*TP*CP*AP*CP*GP*CP*AP*CP*GP*TP*C)-3'
C: 5'-D(*GP*AP*CP*GP*TP*AP*CP*GP*TP*GP*AP*TP*CP*GP*CP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,9949
Polymers76,9963
Non-polymers9976
Water12,070670
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6310 Å2
ΔGint-52 kcal/mol
Surface area30100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.750, 93.840, 105.770
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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DNA chain , 2 types, 2 molecules BC

#2: DNA chain 5'-D(*GP*CP*GP*AP*TP*CP*AP*CP*GP*CP*AP*CP*GP*TP*C)-3'


Mass: 4554.962 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Primer Strand
#3: DNA chain 5'-D(*GP*AP*CP*GP*TP*AP*CP*GP*TP*GP*AP*TP*CP*GP*CP*A)-3'


Mass: 4923.204 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Template Strand

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Protein / Sugars , 2 types, 3 molecules A

#1: Protein DNA polymerase I


Mass: 67518.297 Da / Num. of mol.: 1 / Fragment: Bacillus Fragment (UNP residues 285-876)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus (bacteria) / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: C9RTX7, DNA-directed DNA polymerase
#4: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 3 types, 674 molecules

#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 670 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE AUTHORS STATE THAT THE GEOBACILLUS SP. STRAIN IS UNKNOWN BUT SIMILAR TO Y412MC61.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 56.5 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 45-50% saturated ammonium sulfate, 2.5% MPD, 10 mM magnesium sulfate, 100 mM MES, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 29, 2009
RadiationMonochromator: Rosenbaum-Rock double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 115264 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.043 / Net I/σ(I): 22.16
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.6-1.70.4973.77199.2
1.7-1.810.2756.641100
1.81-1.960.15611.011100
1.96-2.140.08218.951100
2.14-2.40.05327.081100
2.4-2.770.0434.611100
2.77-3.380.03144.51100
3.38-4.770.02852.91199.9
4.77-500.02853.21198.9

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1L3V

1l3v


Resolution: 1.6→45.295 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.33 / σ(F): 2.35 / Phase error: 19.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1923 4871 4.39 %
Rwork0.1778 --
obs0.1785 111078 96.18 %
Solvent computationShrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.952 Å2 / ksol: 0.444 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.5439 Å2-0 Å2-0 Å2
2---2.831 Å20 Å2
3----1.7129 Å2
Refinement stepCycle: LAST / Resolution: 1.6→45.295 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4654 629 62 670 6015
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015533
X-RAY DIFFRACTIONf_angle_d1.297625
X-RAY DIFFRACTIONf_dihedral_angle_d17.1162127
X-RAY DIFFRACTIONf_chiral_restr0.103865
X-RAY DIFFRACTIONf_plane_restr0.006872
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.61820.25071580.23943016X-RAY DIFFRACTION83
1.6182-1.63720.22721660.22743143X-RAY DIFFRACTION88
1.6372-1.65720.23521720.21353274X-RAY DIFFRACTION90
1.6572-1.67820.24451710.20823238X-RAY DIFFRACTION90
1.6782-1.70030.20981730.20343296X-RAY DIFFRACTION91
1.7003-1.72350.21781150.19143383X-RAY DIFFRACTION92
1.7235-1.74820.2211090.1893448X-RAY DIFFRACTION93
1.7482-1.77430.19491130.18863422X-RAY DIFFRACTION93
1.7743-1.8020.2361070.19073501X-RAY DIFFRACTION94
1.802-1.83150.22671200.193553X-RAY DIFFRACTION95
1.8315-1.86310.18591250.1873517X-RAY DIFFRACTION95
1.8631-1.8970.20311540.18273470X-RAY DIFFRACTION96
1.897-1.93350.18791430.17843577X-RAY DIFFRACTION97
1.9335-1.97290.17611560.17733585X-RAY DIFFRACTION98
1.9729-2.01580.18791760.17823564X-RAY DIFFRACTION98
2.0158-2.06270.19531580.17023612X-RAY DIFFRACTION99
2.0627-2.11430.17331910.16483627X-RAY DIFFRACTION99
2.1143-2.17150.17821620.16533593X-RAY DIFFRACTION99
2.1715-2.23540.19421640.15923642X-RAY DIFFRACTION99
2.2354-2.30750.17451760.15693654X-RAY DIFFRACTION99
2.3075-2.390.15911490.16553660X-RAY DIFFRACTION99
2.39-2.48570.18541840.16953669X-RAY DIFFRACTION99
2.4857-2.59880.17951810.17583657X-RAY DIFFRACTION100
2.5988-2.73580.21622000.17763648X-RAY DIFFRACTION100
2.7358-2.90720.20581700.18493686X-RAY DIFFRACTION100
2.9072-3.13160.2012020.18713710X-RAY DIFFRACTION100
3.1316-3.44660.19441690.18143706X-RAY DIFFRACTION100
3.4466-3.94510.1791930.16623734X-RAY DIFFRACTION100
3.9451-4.96950.17792230.15563728X-RAY DIFFRACTION100
4.9695-45.3130.20451910.20383894X-RAY DIFFRACTION99

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